In this report, we extract information about published JOSS papers and generate graphics as well as a summary table that can be downloaded and used for further analyses.
suppressPackageStartupMessages({
library(tibble)
library(rcrossref)
library(dplyr)
library(tidyr)
library(ggplot2)
library(lubridate)
library(gh)
library(purrr)
library(jsonlite)
library(DT)
library(plotly)
library(citecorp)
library(readr)
})## Keep track of the source of each column
source_track <- c()
## Determine whether to add a caption with today's date to the (non-interactive) plots
add_date_caption <- TRUE
if (add_date_caption) {
dcap <- lubridate::today()
} else {
dcap <- ""
}## Read archived version of summary data frame, to use for filling in
## information about software repositories (due to limit on API requests)
## Sort by the date when software repo info was last obtained
papers_archive <- readRDS(gzcon(url("https://github.com/openjournals/joss-analytics/blob/gh-pages/joss_submission_analytics.rds?raw=true"))) %>%
dplyr::arrange(!is.na(repo_info_obtained), repo_info_obtained)
## Similarly for citation analysis, to avoid having to pull down the
## same information multiple times
citations_archive <- readr::read_delim(
url("https://github.com/openjournals/joss-analytics/blob/gh-pages/joss_submission_citations.tsv?raw=true"),
col_types = cols(.default = "c"), col_names = TRUE,
delim = "\t")We get the information about published JOSS papers from Crossref, using the rcrossref R package. This package is also used to extract citation counts.
## Fetch JOSS papers from Crossref
## Only 1000 papers at the time can be pulled down
lim <- 1000
papers <- rcrossref::cr_works(filter = c(issn = "2475-9066"),
limit = lim)$data
i <- 1
while (nrow(papers) == i * lim) {
papers <- dplyr::bind_rows(
papers,
rcrossref::cr_works(filter = c(issn = "2475-9066"),
limit = lim, offset = i * lim)$data)
i <- i + 1
}
papers <- papers %>%
dplyr::filter(type == "journal-article")
## A few papers don't have DOIs - generate them from the URL
noaltid <- which(is.na(papers$alternative.id))
papers$alternative.id[noaltid] <- gsub("http://dx.doi.org/", "",
papers$url[noaltid])
## Get citation info from Crossref and merge with paper details
cit <- rcrossref::cr_citation_count(doi = papers$alternative.id)
papers <- papers %>% dplyr::left_join(
cit %>% dplyr::rename(citation_count = count),
by = c("alternative.id" = "doi")
)
## Remove one duplicated paper
papers <- papers %>% dplyr::filter(alternative.id != "10.21105/joss.00688")
source_track <- c(source_track,
structure(rep("crossref", ncol(papers)),
names = colnames(papers)))For each published paper, we use the Whedon API to get information about pre-review and review issue numbers, corresponding software repository etc.
whedon <- list()
p <- 1
a <- jsonlite::fromJSON(
url(paste0("https://joss.theoj.org/papers/published.json?page=", p)),
simplifyDataFrame = FALSE
)
while (length(a) > 0) {
whedon <- c(whedon, a)
p <- p + 1
a <- jsonlite::fromJSON(
url(paste0("https://joss.theoj.org/papers/published.json?page=", p)),
simplifyDataFrame = FALSE
)
}
whedon <- do.call(dplyr::bind_rows, lapply(whedon, function(w) {
data.frame(api_title = w$title,
api_state = w$state,
editor = paste(w$metadata$paper$editor, collapse = ","),
reviewers = paste(w$reviewers, collapse = ","),
nbr_reviewers = length(w$reviewers),
repo_url = w$repository_url,
review_issue_id = w$review_issue_id,
doi = w$doi,
prereview_issue_id = ifelse(!is.null(w$meta_review_issue_id),
w$meta_review_issue_id, NA_integer_),
languages = paste(w$metadata$paper$languages, collapse = ","),
archive_doi = w$metadata$paper$archive_doi)
}))
papers <- papers %>% dplyr::left_join(whedon, by = c("alternative.id" = "doi"))
source_track <- c(source_track,
structure(rep("whedon", length(setdiff(colnames(papers),
names(source_track)))),
names = setdiff(colnames(papers), names(source_track))))From each pre-review and review issue, we extract information about review times and assigned labels.
## Pull down info on all issues in the joss-reviews repository
issues <- gh("/repos/openjournals/joss-reviews/issues",
.limit = 5000, state = "all")## From each issue, extract required information
iss <- do.call(dplyr::bind_rows, lapply(issues, function(i) {
data.frame(title = i$title,
number = i$number,
state = i$state,
opened = i$created_at,
closed = ifelse(!is.null(i$closed_at),
i$closed_at, NA_character_),
ncomments = i$comments,
labels = paste(setdiff(
vapply(i$labels, getElement,
name = "name", character(1L)),
c("review", "pre-review", "query-scope", "paused")),
collapse = ","))
}))
## Split into REVIEW, PRE-REVIEW, and other issues (the latter category
## is discarded)
issother <- iss %>% dplyr::filter(!grepl("\\[PRE REVIEW\\]", title) &
!grepl("\\[REVIEW\\]", title))
dim(issother)## [1] 66 7
## title
## 1 Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
## 2 Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
## 3 License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
## 4 Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
## 5 Contribution and authorship: Has the submitting author (@rlonka) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
## 6 A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
## number state opened closed ncomments labels
## 1 3600 closed 2021-08-10T19:53:29Z 2021-08-10T19:53:32Z 1
## 2 3599 closed 2021-08-10T19:46:56Z 2021-08-10T19:46:59Z 2
## 3 3591 closed 2021-08-09T09:03:56Z 2021-08-09T09:04:12Z 1
## 4 3589 closed 2021-08-09T08:10:53Z 2021-08-09T08:12:00Z 1
## 5 3577 closed 2021-08-06T09:04:49Z 2021-08-06T09:07:42Z 4
## 6 3573 closed 2021-08-05T07:53:59Z 2021-08-05T12:06:12Z 6
## For REVIEW issues, generate the DOI of the paper from the issue number
getnbrzeros <- function(s) {
paste(rep(0, 5 - nchar(s)), collapse = "")
}
issrev <- iss %>% dplyr::filter(grepl("\\[REVIEW\\]", title)) %>%
dplyr::mutate(nbrzeros = purrr::map_chr(number, getnbrzeros)) %>%
dplyr::mutate(alternative.id = paste0("10.21105/joss.",
nbrzeros,
number)) %>%
dplyr::select(-nbrzeros) %>%
dplyr::mutate(title = gsub("\\[REVIEW\\]: ", "", title)) %>%
dplyr::rename_at(vars(-alternative.id), ~ paste0("review_", .))## For pre-review and review issues, respectively, get the number of
## issues closed each month, and the number of those that have the
## 'rejected' label
review_rejected <- iss %>%
dplyr::filter(grepl("\\[REVIEW\\]", title)) %>%
dplyr::filter(!is.na(closed)) %>%
dplyr::mutate(closedmonth = lubridate::floor_date(as.Date(closed), "month")) %>%
dplyr::group_by(closedmonth) %>%
dplyr::summarize(nbr_issues_closed = length(labels),
nbr_rejections = sum(grepl("rejected", labels))) %>%
dplyr::mutate(itype = "review")
prereview_rejected <- iss %>%
dplyr::filter(grepl("\\[PRE REVIEW\\]", title)) %>%
dplyr::filter(!is.na(closed)) %>%
dplyr::mutate(closedmonth = lubridate::floor_date(as.Date(closed), "month")) %>%
dplyr::group_by(closedmonth) %>%
dplyr::summarize(nbr_issues_closed = length(labels),
nbr_rejections = sum(grepl("rejected", labels))) %>%
dplyr::mutate(itype = "pre-review")
all_rejected <- dplyr::bind_rows(review_rejected, prereview_rejected)## For PRE-REVIEW issues, add information about the corresponding REVIEW
## issue number
isspre <- iss %>% dplyr::filter(grepl("\\[PRE REVIEW\\]", title)) %>%
dplyr::filter(!grepl("withdrawn", labels)) %>%
dplyr::filter(!grepl("rejected", labels))
## Some titles have multiple pre-review issues. In these cases, keep the latest
isspre <- isspre %>% dplyr::arrange(desc(number)) %>%
dplyr::filter(!duplicated(title)) %>%
dplyr::mutate(title = gsub("\\[PRE REVIEW\\]: ", "", title)) %>%
dplyr::rename_all(~ paste0("prerev_", .))
papers <- papers %>% dplyr::left_join(issrev, by = "alternative.id") %>%
dplyr::left_join(isspre, by = c("prereview_issue_id" = "prerev_number")) %>%
dplyr::mutate(prerev_opened = as.Date(prerev_opened),
prerev_closed = as.Date(prerev_closed),
review_opened = as.Date(review_opened),
review_closed = as.Date(review_closed)) %>%
dplyr::mutate(days_in_pre = prerev_closed - prerev_opened,
days_in_rev = review_closed - review_opened,
to_review = !is.na(review_opened))
source_track <- c(source_track,
structure(rep("joss-github", length(setdiff(colnames(papers),
names(source_track)))),
names = setdiff(colnames(papers), names(source_track))))## Reorder so that software repositories that were interrogated longest
## ago are checked first
tmporder <- order(match(papers$alternative.id, papers_archive$alternative.id),
na.last = FALSE)
software_urls <- papers$repo_url[tmporder]
is_github <- grepl("github", software_urls)
length(is_github)## [1] 1341
## [1] 1273
## [1] "https://bitbucket.org/berkeleylab/esdr-pygdh/"
## [2] "https://bitbucket.org/cloopsy/android/"
## [3] "https://bitbucket.org/glotzer/rowan"
## [4] "https://earth.bsc.es/gitlab/wuruchi/autosubmitreact"
## [5] "https://bitbucket.org/miketuri/perl-spice-sim-seus/"
## [6] "https://gitlab.com/libreumg/dataquier.git"
## [7] "https://gitlab.com/moorepants/skijumpdesign"
## [8] "https://gitlab.com/toposens/public/ros-packages"
## [9] "https://bitbucket.org/basicsums/basicsums"
## [10] "https://savannah.nongnu.org/projects/complot/"
## [11] "https://bitbucket.org/cardosan/brightway2-temporalis"
## [12] "https://bitbucket.org/cdegroot/wediff"
## [13] "https://gitlab.com/costrouc/pysrim"
## [14] "https://gitlab.com/materials-modeling/wulffpack"
## [15] "https://gitlab.com/davidtourigny/dynamic-fba"
## [16] "https://gitlab.com/QComms/cqptoolkit"
## [17] "https://gitlab.com/dlr-dw/ontocode"
## [18] "https://gitlab.com/eidheim/Simple-Web-Server"
## [19] "https://bitbucket.org/dghoshal/frieda"
## [20] "https://gitlab.com/mmartin-lagarde/exonoodle-exoplanets/-/tree/master/"
## [21] "https://framagit.org/GustaveCoste/eldam"
## [22] "https://c4science.ch/source/tamaas/"
## [23] "https://gitlab.com/tesch1/cppduals"
## [24] "https://gitlab.com/gdetor/genetic_alg"
## [25] "https://doi.org/10.17605/OSF.IO/3DS6A"
## [26] "https://bitbucket.org/hammurabicode/hamx"
## [27] "https://gitlab.com/datafold-dev/datafold/"
## [28] "https://bitbucket.org/meg/cbcbeat"
## [29] "https://gitlab.gwdg.de/mpievolbio-it/crbhits"
## [30] "https://bitbucket.org/mpi4py/mpi4py-fft"
## [31] "https://gitlab.inria.fr/bramas/tbfmm"
## [32] "https://gitlab.inria.fr/miet/miet"
## [33] "https://bitbucket.org/ocellarisproject/ocellaris"
## [34] "https://gitlab.com/ffaucher/hawen"
## [35] "https://bitbucket.org/sciencecapsule/sciencecapsule"
## [36] "https://bitbucket.org/rram/dvrlib/src/joss/"
## [37] "http://mutabit.com/repos.fossil/grafoscopio/"
## [38] "https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie"
## [39] "https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/"
## [40] "https://ts-gitlab.iup.uni-heidelberg.de/utopia/utopia"
## [41] "https://ts-gitlab.iup.uni-heidelberg.de/utopia/dantro"
## [42] "https://gitlab.inria.fr/mosaic/bvpy"
## [43] "https://gitlab.com/project-dare/dare-platform"
## [44] "https://gitlab.com/cosmograil/PyCS3"
## [45] "https://git.iws.uni-stuttgart.de/tools/frackit"
## [46] "https://bitbucket.org/likask/mofem-cephas"
## [47] "https://gitlab.com/energyincities/besos/"
## [48] "https://gitlab.com/geekysquirrel/bigx"
## [49] "https://bitbucket.org/clhaley/Multitaper.jl"
## [50] "https://gitlab.com/gims-developers/gims"
## [51] "https://gitlab.com/sails-dev/sails"
## [52] "https://gitlab.com/LMSAL_HUB/aia_hub/aiapy"
## [53] "https://git.rwth-aachen.de/ants/sensorlab/imea"
## [54] "https://gitlab.inria.fr/azais/treex"
## [55] "https://gitlab.com/fduchate/predihood"
## [56] "https://gitlab.ethz.ch/holukas/dyco-dynamic-lag-compensation"
## [57] "https://bitbucket.org/dolfin-adjoint/pyadjoint"
## [58] "https://gitlab.com/cerfacs/batman"
## [59] "https://gitlab.com/celliern/scikit-fdiff/"
## [60] "https://gitlab.com/emd-dev/emd"
## [61] "https://www.idpoisson.fr/fullswof/"
## [62] "https://bitbucket.org/manuela_s/hcp/"
## [63] "https://gitlab.com/ampere2/metalwalls"
## [64] "https://sourceforge.net/p/mcapl/mcapl_code/ci/master/tree/"
## [65] "https://gitlab.com/vibes-developers/vibes"
## [66] "https://gitlab.com/myqueue/myqueue"
## [67] "https://bitbucket.org/cmutel/brightway2"
## [68] "https://gitlab.com/dlr-ve/autumn/"
df <- do.call(dplyr::bind_rows, lapply(software_urls[is_github], function(u) {
u0 <- gsub("^http://", "https://", gsub("\\.git$", "", gsub("/$", "", u)))
if (grepl("/tree/", u0)) {
u0 <- strsplit(u0, "/tree/")[[1]][1]
}
if (grepl("/blob/", u0)) {
u0 <- strsplit(u0, "/blob/")[[1]][1]
}
info <- try({
gh(gsub("(https://)?(www.)?github.com/", "/repos/", u0))
})
languages <- try({
gh(paste0(gsub("(https://)?(www.)?github.com/", "/repos/", u0), "/languages"),
.limit = 500)
})
topics <- try({
gh(paste0(gsub("(https://)?(www.)?github.com/", "/repos/", u0), "/topics"),
.accept = "application/vnd.github.mercy-preview+json", .limit = 500)
})
contribs <- try({
gh(paste0(gsub("(https://)?(www.)?github.com/", "/repos/", u0), "/contributors"),
.limit = 500)
})
if (!is(info, "try-error") && length(info) > 1) {
if (!is(contribs, "try-error")) {
if (length(contribs) == 0) {
repo_nbr_contribs <- repo_nbr_contribs_2ormore <- NA_integer_
} else {
repo_nbr_contribs <- length(contribs)
repo_nbr_contribs_2ormore <- sum(vapply(contribs, function(x) x$contributions >= 2, NA_integer_))
if (is.na(repo_nbr_contribs_2ormore)) {
print(contribs)
}
}
} else {
repo_nbr_contribs <- repo_nbr_contribs_2ormore <- NA_integer_
}
if (!is(languages, "try-error")) {
if (length(languages) == 0) {
repolang <- ""
} else {
repolang <- paste(paste(names(unlist(languages)),
unlist(languages), sep = ":"), collapse = ",")
}
} else {
repolang <- ""
}
if (!is(topics, "try-error")) {
if (length(topics$names) == 0) {
repotopics <- ""
} else {
repotopics <- paste(unlist(topics$names), collapse = ",")
}
} else {
repotopics <- ""
}
data.frame(repo_url = u,
repo_created = info$created_at,
repo_updated = info$updated_at,
repo_pushed = info$pushed_at,
repo_nbr_stars = info$stargazers_count,
repo_language = ifelse(!is.null(info$language),
info$language, NA_character_),
repo_languages_bytes = repolang,
repo_topics = repotopics,
repo_license = ifelse(!is.null(info$license),
info$license$key, NA_character_),
repo_nbr_contribs = repo_nbr_contribs,
repo_nbr_contribs_2ormore = repo_nbr_contribs_2ormore
)
} else {
NULL
}
})) %>%
dplyr::mutate(repo_created = as.Date(repo_created),
repo_updated = as.Date(repo_updated),
repo_pushed = as.Date(repo_pushed)) %>%
dplyr::distinct() %>%
dplyr::mutate(repo_info_obtained = lubridate::today())
stopifnot(length(unique(df$repo_url)) == length(df$repo_url))
dim(df)
## For papers not in df (i.e., for which we didn't get a valid response
## from the GitHub API query), use information from the archived data frame
dfarchive <- papers_archive %>%
dplyr::select(colnames(df)[colnames(df) %in% colnames(papers_archive)]) %>%
dplyr::filter(!(repo_url %in% df$repo_url))
df <- dplyr::bind_rows(df, dfarchive)
papers <- papers %>% dplyr::left_join(df, by = "repo_url")
source_track <- c(source_track,
structure(rep("sw-github", length(setdiff(colnames(papers),
names(source_track)))),
names = setdiff(colnames(papers), names(source_track))))## Convert publication date to Date format
## Add information about the half year (H1, H2) of publication
## Count number of authors
papers <- papers %>% dplyr::select(-reference, -license, -link) %>%
dplyr::mutate(published.date = as.Date(published.print)) %>%
dplyr::mutate(
halfyear = paste0(year(published.date),
ifelse(month(published.date) <= 6, "H1", "H2"))
) %>% dplyr::mutate(
halfyear = factor(halfyear,
levels = paste0(rep(sort(unique(year(published.date))),
each = 2), c("H1", "H2")))
) %>% dplyr::mutate(nbr_authors = vapply(author, function(a) nrow(a), NA_integer_))
papers <- papers %>% dplyr::distinct()
source_track <- c(source_track,
structure(rep("cleanup", length(setdiff(colnames(papers),
names(source_track)))),
names = setdiff(colnames(papers), names(source_track))))In some cases, fetching information from (e.g.) the GitHub API fails for a subset of the publications. There are also other reasons for missing values (for example, the earliest submissions do not have an associated pre-review issue). The table below lists the number of missing values for each of the variables in the data frame.
ggplot(papers %>%
dplyr::mutate(pubmonth = lubridate::floor_date(published.date, "month")) %>%
dplyr::group_by(pubmonth) %>%
dplyr::summarize(npub = n()),
aes(x = factor(pubmonth), y = npub)) +
geom_bar(stat = "identity") + theme_minimal() +
labs(x = "", y = "Number of published papers per month", caption = dcap) +
theme(axis.title = element_text(size = 15),
axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))ggplot(papers %>%
dplyr::mutate(pubyear = lubridate::year(published.date)) %>%
dplyr::group_by(pubyear) %>%
dplyr::summarize(npub = n()),
aes(x = factor(pubyear), y = npub)) +
geom_bar(stat = "identity") + theme_minimal() +
labs(x = "", y = "Number of published papers per year", caption = dcap) +
theme(axis.title = element_text(size = 15),
axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))The plots below illustrate the fraction of pre-review and review issues closed during each month that have the ‘rejected’ label attached.
ggplot(all_rejected,
aes(x = factor(closedmonth), y = nbr_rejections/nbr_issues_closed)) +
geom_bar(stat = "identity") +
theme_minimal() +
facet_wrap(~ itype, ncol = 1) +
labs(x = "Month of issue closing", y = "Fraction of issues rejected",
caption = dcap) +
theme(axis.title = element_text(size = 15),
axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))Papers with 20 or more citations are grouped in the “>=20” category.
ggplot(papers %>%
dplyr::mutate(citation_count = replace(citation_count,
citation_count >= 20, ">=20")) %>%
dplyr::mutate(citation_count = factor(citation_count,
levels = c(0:20, ">=20"))) %>%
dplyr::group_by(citation_count) %>%
dplyr::tally(),
aes(x = citation_count, y = n)) +
geom_bar(stat = "identity") +
theme_minimal() +
labs(x = "Crossref citation count", y = "Number of publications", caption = dcap)The table below sorts the JOSS papers in decreasing order by the number of citations in Crossref.
DT::datatable(
papers %>%
dplyr::mutate(url = paste0("<a href='", url, "' target='_blank'>",
url,"</a>")) %>%
dplyr::arrange(desc(citation_count)) %>%
dplyr::select(title, url, published.date, citation_count),
escape = FALSE,
filter = list(position = 'top', clear = FALSE),
options = list(scrollX = TRUE)
)plotly::ggplotly(
ggplot(papers, aes(x = published.date, y = citation_count, label = title)) +
geom_point(alpha = 0.5) + theme_bw() + scale_y_sqrt() +
geom_smooth() +
labs(x = "Date of publication", y = "Crossref citation count", caption = dcap) +
theme(axis.title = element_text(size = 15)),
tooltip = c("label", "x", "y")
)Here, we plot the citation count for all papers published within each half year, sorted in decreasing order.
ggplot(papers %>% dplyr::group_by(halfyear) %>%
dplyr::arrange(desc(citation_count)) %>%
dplyr::mutate(idx = seq_along(citation_count)),
aes(x = idx, y = citation_count)) +
geom_point(alpha = 0.5) +
facet_wrap(~ halfyear, scales = "free") +
theme_bw() +
labs(x = "Index", y = "Crossref citation count", caption = dcap)In these plots we investigate whether the time a submission spends in the pre-review or review stage has changed over time.
ggplot(papers, aes(x = prerev_opened, y = as.numeric(days_in_pre))) +
geom_point() + geom_smooth() + theme_bw() +
labs(x = "Date of pre-review opening", y = "Number of days in pre-review",
caption = dcap) +
theme(axis.title = element_text(size = 15))ggplot(papers, aes(x = review_opened, y = as.numeric(days_in_rev))) +
geom_point() + geom_smooth() + theme_bw() +
labs(x = "Date of review opening", y = "Number of days in review",
caption = dcap) +
theme(axis.title = element_text(size = 15))Next, we consider the languages used by the submissions, both as reported by Whedon and based on the information encoded in available GitHub repositories (for the latter, we also record the number of bytes of code written in each language). Note that a given submission can use multiple languages.
## Language information from Whedon
sspl <- strsplit(papers$languages, ",")
all_languages <- unique(unlist(sspl))
langs <- do.call(dplyr::bind_rows, lapply(all_languages, function(l) {
data.frame(language = l,
nbr_submissions_Whedon = sum(vapply(sspl, function(v) l %in% v, 0)))
}))
## Language information from GitHub software repos
a <- lapply(strsplit(papers$repo_languages_bytes, ","), function(w) strsplit(w, ":"))
a <- a[sapply(a, length) > 0]
langbytes <- as.data.frame(t(as.data.frame(a))) %>%
setNames(c("language", "bytes")) %>%
dplyr::mutate(bytes = as.numeric(bytes)) %>%
dplyr::filter(!is.na(language)) %>%
dplyr::group_by(language) %>%
dplyr::summarize(nbr_bytes_GitHub = sum(bytes),
nbr_repos_GitHub = length(bytes)) %>%
dplyr::arrange(desc(nbr_bytes_GitHub))
langs <- dplyr::full_join(langs, langbytes, by = "language")ggplot(langs %>% dplyr::arrange(desc(nbr_submissions_Whedon)) %>%
dplyr::filter(nbr_submissions_Whedon > 10) %>%
dplyr::mutate(language = factor(language, levels = language)),
aes(x = language, y = nbr_submissions_Whedon)) +
geom_bar(stat = "identity") +
theme_bw() +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
labs(x = "", y = "Number of submissions", caption = dcap) +
theme(axis.title = element_text(size = 15))DT::datatable(
langs %>% dplyr::arrange(desc(nbr_bytes_GitHub)),
escape = FALSE,
filter = list(position = 'top', clear = FALSE),
options = list(scrollX = TRUE)
)ggplot(langs, aes(x = nbr_repos_GitHub, y = nbr_bytes_GitHub)) +
geom_point() + scale_x_log10() + scale_y_log10() + geom_smooth() +
theme_bw() +
labs(x = "Number of repos using the language",
y = "Total number of bytes of code\nwritten in the language",
caption = dcap) +
theme(axis.title = element_text(size = 15))ggplotly(
ggplot(papers, aes(x = citation_count, y = repo_nbr_stars,
label = title)) +
geom_point(alpha = 0.5) + scale_x_sqrt() + scale_y_sqrt() +
theme_bw() +
labs(x = "Crossref citation count", y = "Number of stars, GitHub repo",
caption = dcap) +
theme(axis.title = element_text(size = 15)),
tooltip = c("label", "x", "y")
)ggplot(papers, aes(x = as.numeric(prerev_opened - repo_created))) +
geom_histogram(bins = 50) +
theme_bw() +
labs(x = "Time (days) from repo creation to JOSS pre-review start",
caption = dcap) +
theme(axis.title = element_text(size = 15))ggplot(papers, aes(x = as.numeric(repo_pushed - review_closed))) +
geom_histogram(bins = 50) +
theme_bw() +
labs(x = "Time (days) from closure of JOSS review to most recent commit in repo",
caption = dcap) +
theme(axis.title = element_text(size = 15)) +
facet_wrap(~ year(published.date), scales = "free_y")Submissions associated with rOpenSci and pyOpenSci are not considered here, since they are not explicitly reviewed at JOSS.
ggplot(papers %>%
dplyr::filter(!grepl("rOpenSci|pyOpenSci", prerev_labels)) %>%
dplyr::mutate(year = year(published.date)),
aes(x = nbr_reviewers)) + geom_bar() +
facet_wrap(~ year) + theme_bw() +
labs(x = "Number of reviewers", y = "Number of submissions", caption = dcap)Submissions associated with rOpenSci and pyOpenSci are not considered here, since they are not explicitly reviewed at JOSS.
reviewers <- papers %>%
dplyr::filter(!grepl("rOpenSci|pyOpenSci", prerev_labels)) %>%
dplyr::mutate(year = year(published.date)) %>%
dplyr::select(reviewers, year) %>%
tidyr::separate_rows(reviewers, sep = ",")
## Most active reviewers
DT::datatable(
reviewers %>% dplyr::group_by(reviewers) %>%
dplyr::summarize(nbr_reviews = length(year),
timespan = paste(unique(c(min(year), max(year))),
collapse = " - ")) %>%
dplyr::arrange(desc(nbr_reviews)),
escape = FALSE, rownames = FALSE,
filter = list(position = 'top', clear = FALSE),
options = list(scrollX = TRUE)
)ggplot(papers %>%
dplyr::mutate(year = year(published.date),
`r/pyOpenSci` = factor(
grepl("rOpenSci|pyOpenSci", prerev_labels),
levels = c("TRUE", "FALSE"))),
aes(x = editor)) + geom_bar(aes(fill = `r/pyOpenSci`)) +
theme_bw() + facet_wrap(~ year, ncol = 1) +
scale_fill_manual(values = c(`TRUE` = "grey65", `FALSE` = "grey35")) +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
labs(x = "Editor", y = "Number of submissions", caption = dcap)all_licenses <- sort(unique(papers$repo_license))
license_levels = c(grep("apache", all_licenses, value = TRUE),
grep("bsd", all_licenses, value = TRUE),
grep("mit", all_licenses, value = TRUE),
grep("gpl", all_licenses, value = TRUE),
grep("mpl", all_licenses, value = TRUE))
license_levels <- c(license_levels, setdiff(all_licenses, license_levels))
ggplot(papers %>%
dplyr::mutate(repo_license = factor(repo_license,
levels = license_levels)),
aes(x = repo_license)) +
geom_bar() +
theme_bw() +
labs(x = "Software license", y = "Number of submissions", caption = dcap) +
theme(axis.title = element_text(size = 15),
axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
facet_wrap(~ year(published.date), scales = "free_y")## For plots below, replace licenses present in less
## than 2.5% of the submissions by 'other'
tbl <- table(papers$repo_license)
to_replace <- names(tbl[tbl <= 0.025 * nrow(papers)])ggplot(papers %>%
dplyr::mutate(year = year(published.date)) %>%
dplyr::mutate(repo_license = replace(repo_license,
repo_license %in% to_replace,
"other")) %>%
dplyr::mutate(year = factor(year),
repo_license = factor(
repo_license,
levels = license_levels[license_levels %in% repo_license]
)) %>%
dplyr::group_by(year, repo_license, .drop = FALSE) %>%
dplyr::count() %>%
dplyr::mutate(year = as.integer(as.character(year))),
aes(x = year, y = n, fill = repo_license)) + geom_area() +
theme_minimal() +
scale_fill_brewer(palette = "Set1", name = "Software\nlicense",
na.value = "grey") +
theme(axis.title = element_text(size = 15)) +
labs(x = "Year", y = "Number of submissions", caption = dcap)ggplot(papers %>%
dplyr::mutate(year = year(published.date)) %>%
dplyr::mutate(repo_license = replace(repo_license,
repo_license %in% to_replace,
"other")) %>%
dplyr::mutate(year = factor(year),
repo_license = factor(
repo_license,
levels = license_levels[license_levels %in% repo_license]
)) %>%
dplyr::group_by(year, repo_license, .drop = FALSE) %>%
dplyr::summarize(n = n()) %>%
dplyr::mutate(freq = n/sum(n)) %>%
dplyr::mutate(year = as.integer(as.character(year))),
aes(x = year, y = freq, fill = repo_license)) + geom_area() +
theme_minimal() +
scale_fill_brewer(palette = "Set1", name = "Software\nlicense",
na.value = "grey") +
theme(axis.title = element_text(size = 15)) +
labs(x = "Year", y = "Fraction of submissions", caption = dcap)a <- unlist(strsplit(papers$repo_topics, ","))
a <- a[!is.na(a)]
topicfreq <- table(a)
colors <- viridis::viridis(100)
set.seed(1234)
wordcloud::wordcloud(
names(topicfreq), sqrt(topicfreq), min.freq = 1, max.words = 300,
random.order = FALSE, rot.per = 0.05, use.r.layout = FALSE,
colors = colors, scale = c(10, 0.1), random.color = TRUE,
ordered.colors = FALSE, vfont = c("serif", "plain")
)Here, we take a more detailed look at the papers that cite JOSS papers, using data from the Open Citations Corpus.
citations <- citecorp::oc_coci_cites(doi = papers$alternative.id) %>%
dplyr::distinct()
dim(citations)## [1] 6176 7
citations <- citations %>%
dplyr::filter(!(oci %in% citations_archive$oci))
tmpj <- rcrossref::cr_works(dois = unique(citations$citing))$data %>%
dplyr::select(contains("doi"), contains("container.title"), contains("issn"),
contains("type"), contains("publisher"), contains("prefix"))
citations <- citations %>% dplyr::left_join(tmpj, by = c("citing" = "doi"))
## bioRxiv preprints don't have a 'container.title' or 'issn', but we'll assume
## that they can be
## identified from the prefix 10.1101 - set the container.title
## for these records manually; we may or may not want to count these
## (would it count citations twice, both preprint and publication?)
citations$container.title[citations$prefix == "10.1101"] <- "bioRxiv"
## JOSS is represented by 'The Journal of Open Source Software' as well as
## 'Journal of Open Source Software'
citations$container.title[citations$container.title ==
"Journal of Open Source Software"] <-
"The Journal of Open Source Software"
## Remove real self citations (cited DOI = citing DOI)
citations <- citations %>% dplyr::filter(cited != citing)
## Merge with the archive
citations <- dplyr::bind_rows(citations, citations_archive)
write.table(citations, file = "joss_submission_citations.tsv",
row.names = FALSE, col.names = TRUE, sep = "\t", quote = FALSE)## Number of JOSS papers with >0 citations included in this collection
length(unique(citations$cited))## [1] 602
## Number of JOSS papers with >0 citations according to Crossref
length(which(papers$citation_count > 0))## [1] 851
## Number of citations from Open Citations Corpus vs Crossref
df0 <- papers %>% dplyr::select(doi, citation_count) %>%
dplyr::full_join(citations %>% dplyr::group_by(cited) %>%
dplyr::tally() %>%
dplyr::mutate(n = replace(n, is.na(n), 0)),
by = c("doi" = "cited"))## [1] 11627
## [1] 6162
## Ratio of total citation count Open Citations Corpus/Crossref
sum(df0$n, na.rm = TRUE)/sum(df0$citation_count, na.rm = TRUE)## [1] 0.5299733
ggplot(df0, aes(x = citation_count, y = n)) +
geom_abline(slope = 1, intercept = 0) +
geom_point(size = 3, alpha = 0.5) +
labs(x = "Crossref citation count", y = "Open Citations Corpus citation count",
caption = dcap) +
theme_bw()## Zoom in
ggplot(df0, aes(x = citation_count, y = n)) +
geom_abline(slope = 1, intercept = 0) +
geom_point(size = 3, alpha = 0.5) +
labs(x = "Crossref citation count", y = "Open Citations Corpus citation count",
caption = dcap) +
theme_bw() +
coord_cartesian(xlim = c(0, 75), ylim = c(0, 75))## [1] 1902
## [1] 1641
topcit <- citations %>% dplyr::group_by(container.title) %>%
dplyr::summarize(nbr_citations_of_joss_papers = length(cited),
nbr_cited_joss_papers = length(unique(cited)),
nbr_citing_papers = length(unique(citing)),
nbr_selfcitations_of_joss_papers = sum(author_sc == "yes"),
fraction_selfcitations = signif(nbr_selfcitations_of_joss_papers /
nbr_citations_of_joss_papers, digits = 3)) %>%
dplyr::arrange(desc(nbr_cited_joss_papers))
DT::datatable(topcit,
escape = FALSE, rownames = FALSE,
filter = list(position = 'top', clear = FALSE),
options = list(scrollX = TRUE))plotly::ggplotly(
ggplot(topcit, aes(x = nbr_citations_of_joss_papers, y = nbr_cited_joss_papers,
label = container.title)) +
geom_abline(slope = 1, intercept = 0, linetype = "dashed", color = "grey") +
geom_point(size = 3, alpha = 0.5) +
theme_bw() +
labs(caption = dcap, x = "Number of citations of JOSS papers",
y = "Number of cited JOSS papers")
)plotly::ggplotly(
ggplot(topcit, aes(x = nbr_citations_of_joss_papers, y = nbr_cited_joss_papers,
label = container.title)) +
geom_abline(slope = 1, intercept = 0, linetype = "dashed", color = "grey") +
geom_point(size = 3, alpha = 0.5) +
theme_bw() +
coord_cartesian(xlim = c(0, 100), ylim = c(0, 50)) +
labs(caption = dcap, x = "Number of citations of JOSS papers",
y = "Number of cited JOSS papers")
)The tibble object with all data collected above is serialized to a file that can be downloaded and reused.
## alternative.id container.title created deposited
## 1 10.21105/joss.00900 Journal of Open Source Software 2018-09-23 2018-09-23
## 2 10.21105/joss.02581 Journal of Open Source Software 2020-08-26 2020-08-26
## 3 10.21105/joss.01075 Journal of Open Source Software 2019-03-24 2019-03-24
## 4 10.21105/joss.00064 The Journal of Open Source Software 2017-01-12 2017-10-24
## 5 10.21105/joss.01423 Journal of Open Source Software 2019-05-08 2019-11-17
## 6 10.21105/joss.01882 Journal of Open Source Software 2020-03-23 2020-03-23
## published.print doi indexed issn issue issued
## 1 2018-09-23 10.21105/joss.00900 2020-03-10 2475-9066 29 2018-09-23
## 2 2020-08-26 10.21105/joss.02581 2020-08-26 2475-9066 52 2020-08-26
## 3 2019-03-24 10.21105/joss.01075 2021-07-03 2475-9066 35 2019-03-24
## 4 2017-01-12 10.21105/joss.00064 2021-06-23 2475-9066 9 2017-01-12
## 5 2019-05-08 10.21105/joss.01423 2020-04-07 2475-9066 37 2019-05-08
## 6 2020-03-23 10.21105/joss.01882 2021-06-02 2475-9066 47 2020-03-23
## member page prefix publisher score source reference.count
## 1 8722 900 10.21105 The Open Journal 1 Crossref 9
## 2 8722 2581 10.21105 The Open Journal 1 Crossref 10
## 3 8722 1075 10.21105 The Open Journal 1 Crossref 9
## 4 8722 64 10.21105 The Open Journal 1 Crossref 9
## 5 8722 1423 10.21105 The Open Journal 1 Crossref 9
## 6 8722 1882 10.21105 The Open Journal 1 Crossref 13
## references.count is.referenced.by.count
## 1 9 1
## 2 10 0
## 3 9 14
## 4 9 6
## 5 9 1
## 6 13 1
## title
## 1 GB code: A grain boundary generation code
## 2 SALSA: A Python Package for Constructing Synthetic Quasar Absorption Line Catalogs from Astrophysical Hydrodynamic Simulations
## 3 Yellowbrick: Visualizing the Scikit-Learn Model Selection Process
## 4 ecopath_matlab: A Matlab-based implementation of the Ecopath food web algorithm
## 5 CRED: a rapid peak caller for Chem-seq data
## 6 splot - visual analytics for spatial statistics
## type url volume
## 1 journal-article http://dx.doi.org/10.21105/joss.00900 3
## 2 journal-article http://dx.doi.org/10.21105/joss.02581 5
## 3 journal-article http://dx.doi.org/10.21105/joss.01075 4
## 4 journal-article http://dx.doi.org/10.21105/joss.00064 2
## 5 journal-article http://dx.doi.org/10.21105/joss.01423 4
## 6 journal-article http://dx.doi.org/10.21105/joss.01882 5
## short.container.title
## 1 JOSS
## 2 JOSS
## 3 JOSS
## 4 JOSS
## 5 JOSS
## 6 JOSS
## author
## 1 http://orcid.org/0000-0002-9616-4602, http://orcid.org/0000-0003-4281-5665, NA, FALSE, FALSE, NA, R., B., J., Hadian, Grabowski, Neugebauer, first, additional, additional
## 2 http://orcid.org/0000-0003-0872-7098, NA, NA, NA, NA, NA, FALSE, NA, NA, NA, NA, NA, Brendan, Devin, Brian, Jason, Molly, Nicholas, Boyd, Silvia, O’Shea, Tumlinson, Peeples, Earl, first, additional, additional, additional, additional, additional
## 3 http://orcid.org/0000-0003-0660-7682, http://orcid.org/0000-0002-1143-044X, FALSE, FALSE, Benjamin, Rebecca, Bengfort, Bilbro, first, additional
## 4 Kelly, A. Kearney, first
## 5 http://orcid.org/0000-0002-8086-3185, http://orcid.org/0000-0003-2358-7919, http://orcid.org/0000-0002-0916-7339, http://orcid.org/0000-0002-3992-5399, FALSE, FALSE, FALSE, FALSE, Jason, Tony, Paul, Hiroki, Lin, Kuo, Horton, Nagase, first, additional, additional, additional
## 6 http://orcid.org/0000-0002-7007-5812, http://orcid.org/0000-0002-6274-1619, http://orcid.org/0000-0002-1889-5282, http://orcid.org/0000-0002-4776-6826, http://orcid.org/0000-0002-3856-3736, http://orcid.org/0000-0002-1073-7781, http://orcid.org/0000-0002-0537-2941, http://orcid.org/0000-0003-0274-599X, http://orcid.org/0000-0001-5857-9762, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, Stefanie, Dani, Renan, James, Verena, Wei, Taylor, Levi, Sergio, Lumnitz, Arribas-Bell, Cortes, Gaboardi, Griess, Kang, Oshan, Wolf, Rey, first, additional, additional, additional, additional, additional, additional, additional, additional
## content_domain citation_count
## 1 , FALSE 1
## 2 , FALSE 0
## 3 , FALSE 14
## 4 , FALSE 6
## 5 , FALSE 1
## 6 , FALSE 2
## api_title
## 1 GB code: A grain boundary generation code
## 2 SALSA: A Python Package for Constructing Synthetic Quasar Absorption Line Catalogs from Astrophysical Hydrodynamic Simulations
## 3 Yellowbrick: Visualizing the Scikit-Learn Model Selection Process
## 4 ecopath_matlab: A Matlab-based implementation of the Ecopath food web algorithm
## 5 CRED: a rapid peak caller for Chem-seq data
## 6 splot - visual analytics for spatial statistics
## api_state editor reviewers nbr_reviewers
## 1 accepted @labarba @vyasr,@trallard 2
## 2 accepted @danielskatz @olebole,@zpace 2
## 3 accepted @arfon @mnarayan 1
## 4 accepted @Kevin-Mattheus-Moerman @roliveros-ramos 1
## 5 accepted @lpantano @darogan 1
## 6 accepted @leouieda @ResidentMario,@martinfleis 2
## repo_url review_issue_id
## 1 https://github.com/oekosheri/GB_code 900
## 2 https://github.com/biboyd/SALSA 2581
## 3 https://github.com/DistrictDataLabs/yellowbrick 1075
## 4 https://github.com/kakearney/ecopath_matlab-pkg 64
## 5 https://github.com/jlincbio/cred 1423
## 6 https://github.com/pysal/splot 1882
## prereview_issue_id languages
## 1 853 Python,TeX
## 2 2532 Jupyter Notebook,TeX,Shell,Python
## 3 864 Makefile,Python,TeX
## 4 NA Matlab,Python,HTML,TeX
## 5 1374 Makefile,Perl,C,TeX
## 6 1838 Makefile,Jupyter Notebook,TeX,Python
## archive_doi
## 1 https://doi.org/10.5281/zenodo.1433530
## 2 https://doi.org/10.5281/zenodo.4002067
## 3 https://doi.org/10.5281/zenodo.1206239
## 4 http://dx.doi.org/10.5281/zenodo.240977
## 5 https://doi.org/10.5281/zenodo.2667613
## 6 https://doi.org/10.5281/zenodo.3724199
## review_title
## 1 GB_code: A grain boundary generation code
## 2 SALSA: A Python Package for Constructing Synthetic Quasar Absorption Line Catalogs from Astrophysical Hydrodynamic Simulations
## 3 Yellowbrick: Visualizing the Scikit-Learn Model Selection Process
## 4 ecopath_matlab: A Matlab-based implementation of the Ecopath food web algorithm
## 5 CRED: a rapid peak caller for Chem-seq data
## 6 splot: visual analytics for spatial statistics
## review_number review_state review_opened review_closed review_ncomments
## 1 900 closed 2018-08-17 2018-09-23 90
## 2 2581 closed 2020-08-18 2020-08-26 38
## 3 1075 closed 2018-11-11 2019-03-24 41
## 4 64 closed 2016-09-16 2017-01-12 54
## 5 1423 closed 2019-05-01 2019-05-08 93
## 6 1882 closed 2019-11-11 2020-03-23 56
## review_labels
## 1 accepted,recommend-accept,published
## 2 accepted,TeX,Shell,Jupyter Notebook,recommend-accept,published
## 3 accepted,recommend-accept,published
## 4 accepted,recommend-accept,published
## 5 accepted,recommend-accept,published
## 6 accepted,recommend-accept,published
## prerev_title
## 1 GB_code: A grain boundary generation code
## 2 SALSA: A Python Package for Constructing Synthetic Quasar Absorption Line Catalogs from Astrophysical Hydrodynamic Simulations
## 3 Yellowbrick: Visualizing the Scikit-Learn Model Selection Process
## 4 <NA>
## 5 CRED: a rapid peak caller for Chem-seq data
## 6 splot: visual analytics for spatial statistics
## prerev_state prerev_opened prerev_closed prerev_ncomments
## 1 closed 2018-07-26 2018-08-17 42
## 2 closed 2020-07-28 2020-08-18 44
## 3 closed 2018-07-30 2018-11-11 26
## 4 <NA> <NA> <NA> NA
## 5 closed 2019-04-14 2019-05-01 30
## 6 closed 2019-10-28 2019-11-11 28
## prerev_labels days_in_pre days_in_rev to_review repo_created
## 1 TeX,Python 22 days 37 days TRUE 2018-07-12
## 2 TeX,Shell,Jupyter Notebook 21 days 8 days TRUE 2020-06-11
## 3 TeX,Python,Makefile 104 days 133 days TRUE 2016-05-18
## 4 <NA> NA days 118 days TRUE 2016-08-19
## 5 Makefile,C,Perl 17 days 7 days TRUE 2019-04-10
## 6 TeX,Makefile,Jupyter Notebook 14 days 133 days TRUE 2017-04-20
## repo_updated repo_pushed repo_nbr_stars repo_language
## 1 2021-06-11 2019-08-08 24 Python
## 2 2021-01-27 2021-01-12 3 Python
## 3 2021-06-23 2021-05-27 3275 Python
## 4 2019-01-15 2019-01-15 3 MATLAB
## 5 2020-02-26 2020-02-26 1 C
## 6 2021-08-07 2021-08-05 70 Jupyter Notebook
## repo_languages_bytes
## 1 Python:47666,TeX:2712
## 2 Python:97444,Jupyter Notebook:21308,TeX:8559,Shell:546
## 3 Python:1513453,TeX:3743,Makefile:1082
## 4 MATLAB:466188,HTML:181968,TeX:18124,Python:1984
## 5 C:30602,Perl:5262,TeX:3999,Makefile:960
## 6 Jupyter Notebook:2690119,Python:145155,TeX:10299,Makefile:207
## repo_topics
## 1 linear-algebra,crystallography,high-throughput-computing,grain-boundaries,python
## 2
## 3 machine-learning,visual-analysis,model-selection,visualization,scikit-learn,visualizer,matplotlib,python,estimator,anaconda
## 4
## 5
## 6
## repo_license repo_nbr_contribs repo_nbr_contribs_2ormore repo_info_obtained
## 1 mit 2 2 2021-08-07
## 2 bsd-3-clause 2 1 2021-08-07
## 3 apache-2.0 94 44 2021-06-23
## 4 mit 2 2 2021-06-23
## 5 gpl-3.0 2 1 2021-08-07
## 6 bsd-3-clause 38 27 2021-08-07
## published.date halfyear nbr_authors
## 1 2018-09-23 2018H2 3
## 2 2020-08-26 2020H2 6
## 3 2019-03-24 2019H1 2
## 4 2017-01-12 2017H1 1
## 5 2019-05-08 2019H1 4
## 6 2020-03-23 2020H1 9
To read the current version of this file directly from GitHub, use the following code:
## R version 4.1.0 (2021-05-18)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] readr_2.0.1 citecorp_0.3.0 plotly_4.9.4.1 DT_0.18
## [5] jsonlite_1.7.2 purrr_0.3.4 gh_1.3.0 lubridate_1.7.10
## [9] ggplot2_3.3.5 tidyr_1.1.3 dplyr_1.0.7 rcrossref_1.1.0
## [13] tibble_3.1.3
##
## loaded via a namespace (and not attached):
## [1] viridis_0.6.1 httr_1.4.2 sass_0.4.0 splines_4.1.0
## [5] bit64_4.0.5 vroom_1.5.4 viridisLite_0.4.0 bslib_0.2.5.1
## [9] shiny_1.6.0 highr_0.9 triebeard_0.3.0 urltools_1.7.3
## [13] yaml_2.2.1 lattice_0.20-44 pillar_1.6.2 glue_1.4.2
## [17] digest_0.6.27 RColorBrewer_1.1-2 promises_1.2.0.1 colorspace_2.0-2
## [21] Matrix_1.3-3 htmltools_0.5.1.1 httpuv_1.6.1 plyr_1.8.6
## [25] pkgconfig_2.0.3 httpcode_0.3.0 xtable_1.8-4 gitcreds_0.1.1
## [29] scales_1.1.1 whisker_0.4 later_1.2.0 tzdb_0.1.2
## [33] mgcv_1.8-35 generics_0.1.0 farver_2.1.0 ellipsis_0.3.2
## [37] withr_2.4.2 lazyeval_0.2.2 cli_3.0.1 magrittr_2.0.1
## [41] crayon_1.4.1 mime_0.11 evaluate_0.14 fansi_0.5.0
## [45] nlme_3.1-152 xml2_1.3.2 tools_4.1.0 data.table_1.14.0
## [49] hms_1.1.0 lifecycle_1.0.0 stringr_1.4.0 munsell_0.5.0
## [53] compiler_4.1.0 jquerylib_0.1.4 rlang_0.4.11 grid_4.1.0
## [57] htmlwidgets_1.5.3 crosstalk_1.1.1 miniUI_0.1.1.1 labeling_0.4.2
## [61] rmarkdown_2.10 gtable_0.3.0 curl_4.3.2 fauxpas_0.5.0
## [65] R6_2.5.0 gridExtra_2.3 knitr_1.33 fastmap_1.1.0
## [69] bit_4.0.4 utf8_1.2.2 stringi_1.7.3 parallel_4.1.0
## [73] crul_1.1.0 Rcpp_1.0.7 vctrs_0.3.8 wordcloud_2.6
## [77] tidyselect_1.1.1 xfun_0.25